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In a PDF file (or the PDF stream of a .ai file), the text is broken up into lots of small fragments, one or more per line, which makes it hard to edit. We combine the fragments into larger text frames. The checkbox affects how that is done.

Mostly it decides whether to combine multiple lines of text into paragraphs with alignment and wrapping, or leave them as lots of left-aligned single lines with indents. It also affects how precisely individual character positions match the PDF; getting that near perfect involves adding a bit of tracking to each character, and (for larger gaps) potentially adding more tabstops.

The benefit of unchecking the box is the text position should be a near pixel-perfect match to the PDF. The downside is that it may not match what would have happened if you just typed the text by hand; you'll have a lot of spurious tracking changes and tabstops; and, if you edit it, you may have to delete line-breaks to make later lines rewrap.

The downside of checking the box is that you'll usually have small differences in text position due to Affinity's text engine using different justification rules to whatever created the PDF. Sometimes this may cause paragraphs to wrap differently, so words may not be on the same lines. Sometimes the paragraph will end up a line longer or shorter. Whether this matters is something only the user can decide.